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. 2018 Nov 20;13(11):e0207475.
doi: 10.1371/journal.pone.0207475. eCollection 2018.

Diversity across major and candidate genes in European local pig breeds

María Muñoz  1 , Riccardo Bozzi  2 , Fabián García  1 , Yolanda Núñez  1 , Claudia Geraci  3 , Alessandro Crovetti  2 , Juan García-Casco  1 , Estefania Alves  1 , Martin Škrlep  4 , Rui Charneca  5 , Jose M Martins  5 , Raquel Quintanilla  6 , Joan Tibau  6 , Goran Kušec  7 , Ivona Djurkin-Kušec  7 , Marie J Mercat  8 , Juliette Riquet  9 , Jordi Estellé  10 , Christoph Zimmer  11 , Violeta Razmaite  12 , Jose P Araujo  13 , Čedomir Radović  14 , Radomir Savić  15 , Danijel Karolyi  16 , Maurizio Gallo  17 , Marjeta Čandek-Potokar  4 , Luca Fontanesi  3 , Ana I Fernández  1 , Cristina Óvilo  1
Affiliations

Diversity across major and candidate genes in European local pig breeds

María Muñoz et al. PLoS One. .

Abstract

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.

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Conflict of interest statement

The authors have declared that no competing interests exist, excepting that the corresponding author Cristina Óvilo is a PLOS ONE Editorial Board member. However, this does not alter the authors’ adherence to all the PLOS ONE policies.

Figures

Fig 1
Fig 1. Phenotype and geographical origin of the 20 analysed pig breeds: Black Slavonian and Turopolje (Croatia), Basque and Gascon (France), Schwäbisch-Hällisches Schwein (Germany), Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda (Italy), Lithuanian indigenous wattle and Lithuanian White old type (Lithuania), Alentejana and Bísara (Portugal), Moravka and Swallow-Bellied Mangalitsa (Serbia), Krškopolje (Slovenia) and Iberian and Majorcan Black (Spain).
Fig 2
Fig 2
Neighbour-joining tree based on a) Nei’s distances b) FST.
Fig 3
Fig 3. Scatterplot of resulting genetic clusters after Discriminant Analysis of Principal Components for the 20 local European pig breeds.
Fig 4
Fig 4. Membership assignment of the individuals to the a priori clusters defined with DAPC.
Fig 5
Fig 5. Genetic diversity structure of the 20 pig populations.
Population memberships for each genotype is shown based on K = 14 and K = 21.
See this image and copyright information in PMC

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